Dr. Christine Bii, DD CMR

Dr. Christine Bii

Ag. Deputy Director CMR

Dr. Christine C. Bii (PhD) has over 30 years of experience in research in Medical Mycology. Her interest is on opportunistic fungal infections in HIV/AIDS, diabetes, cancer, Aspergillosis in TB and mycotoxins. Her current focus is molecular characterization of Cryptococcus, Candida Spp. and triazole antifungal resistance in Aspergillus spp.

She established research and training in Medical Mycology in KEMRI and her research has contributed to the recognition of fungal infections as a significant cause of morbidity and mortality in immunocompromised individuals. She has authored over 70 manuscripts in peer-reviewed journals and mentored over 60 postgraduate students

Academic /Professional Qualifications
  • PhD Medical Mycology, 2005
  • MSc. Mycology 1998, School of Biological sciences
  • BSc. 1990
Selected Publications
  1. Tonui, J., Mureithi, M., Jaoko, W. and Bii, C. (2020). The spectrum of Filamentous Fungi from Sputum of Tuberculosis Relapse and Retreatment Patients in Tuberculosis Reference Facilities. Open Journal of Medical Microbiology, 10, 190-203.(View)
  2. Mareike Bernhard, Navaporn Worasilchai, Mourine Kangogo, Christine Bii, Wioleta J. Trzaska, Michael Weig, Uwe Groß, Ariya Chindamporn and Oliver Bader. CryptoType – Public Datasets for MALDI-TOF-MS Based Differentiation of Cryptococcus neoformans/gattii Complexes Front. Cell. Infect. Microbiol., 19 April 2021 | (View)
  3. Bii CC, Makimura K, Abe S, Taguchi H, Mugasia OM, Revathi G, Wamae CN, Kamiya S. Serotypes and azole resistance in Cryptococcus neoformans MATα from clinical sources in Nairobi Kenya. Mycoses. 2006; 450:25-30.
  4. Mourine Kangogo, Oliver Bader, Hamadi Boga, Wanjiru Wanyoike, Claudia Folba, Navaporn Worasilchai, Michael Weig, Uwe Groß and Christine C. Bi Molecular types of Cryptococcus gattii/Cryptococcus neoformans species complex from clinical and environmental sources in Nairobi, Kenya. Mycoses;  © 2015 Blackwell Verlag GmbH. (View)
  5. Elizabeth Nyambura Mwaura, Vivian Matiru and Christine Bii. Mycological findings of sputum samples from pulmonary tuberculosis attending TB clinic in Nairobi. Virol Mycol 2013, 2:3 (View)
  6. John A Guto, Christine C Bii, David W Denning. Estimated burden of fungal infections in Kenya. J Infect Dev Ctries 2016; (View)

Prof. Sam Kariuki


Prof. Sam Kariuki is currently th acting Director-General KEMRI and a scientist at the Centre for Microbiology Research at KEMRI in Nairobi and a Wellcome Trust Sanger Institute International Fellow. He is a visiting Professor of Tropical Microbiology, Nuffield Department of Medicine, and the University of Oxford, UK. He is the co-coordinator of the Medical Microbiology Postgraduate course at the Institute of Tropical Medicine and Infectious Diseases, KEMRI.

Prof. Kariuki research interests revolve around epidemiology and antimicrobial resistance of enteric bacterial pathogens, including invasive Non-Typhoidal Salmonellosis (NTS) and typhoid fever, Shigella spp, Vibrio cholerae and Escherichia coli.

He is Chair of Global Antimicrobial Resistance Partnership (GARP)-Kenya chapter and in 2014-16, led the initiative for the development of the Situational Analysis on AMR in Kenya culminating in the National Action Plan Draft document. He has authored/co-authored over 130 papers in peer-reviewed journals and three textbooks on Antimicrobial Resistance and Food Safety.

Selected Publications
  1.  Kariuki S, Dougan G. Antibacterial resistance in sub-Saharan Africa: an underestimated emergency. Ann N Y Acad Sci. 2014; 1323(1):43-55.
  2.  Kariuki S, Revathi G, Kiiru J, et al. Typhoid in Kenya is associated with a dominant Multidrug-Resistant Salmonella enterica Serovar Typhi haplotype that is also widespread in Southeast Asia. J Clin Microbiol. 2010; 48(6):2171-6.
  3. Kariuki S, Revathi G, Kariuki N, Kiiru J, Mwituria J, Muyodi J, Githinji JW, Kagendo D, Munyalo A, Hart CA. Invasive multidrug-resistant non-typhoidal Salmonella infections in Africa: zoonotic or anthroponotic transmission? J Med Microbiol. 2006; 55:585-91.
  4. Kariuki S, Revathi G, Kiiru J, Lowe B, Berkley JA, Hart CA. Decreasing prevalence of antimicrobial resistance in non-typhoidal Salmonella isolated from children with bacteraemia in a rural district hospital, Kenya. Int J Antimicrob Agents. 2006; 28:166 – 171.
  5. Kariuki, S., G. Revathi, N. Kariuki, J. Kiiru, J. Mwituria, Charles A Hart. Characterisation of community-acquired non-typhoidal Salmonella from bacteraemia and diarrhoeal infections in children admitted to hospital in Nairobi, Kenya. BMC Microbiology 2006, 6:101 (15 Dec 2006). PMC1764016

Prof. Elizabeth Bukusi

Senior Principal Clinical Research Scientist

Professor Elizabeth Anne Bukusi (ObGyn), MPH, PhD, PGD (Research Ethics), Masters in Bioethics, Fellow of the African Academy of Sciences, earned her general medical degree and Masters in Obstetrics and Gynecology degree from the University of Nairobi.  She then earned a certificate in international health, MPH and a PhD from the University of Washington’s Department of Epidemiology; a post-graduate diploma in Research Ethics from the University of Cape Town and a Masters in Bioethics from Centre for Bioethics and Culture at the Sind Institute of Urology and Transplantation in Karachi.  She is a certified IRB Professional.

She is a Senior Principal Clinical Research Scientist at the Kenya Medical Research Institute (KEMRI), a Research Professor at the University of Washington (Departments of Obstetrics and Gynecology and Global health), an honorary lecturer at Aga Khan University in Nairobi And Maseno University (Department of Obstetrics and Gynecology) and Volunteer Clinical faculty – Professor at the University of California San Francisco (Department of Obstetrics, Gynecology & Reproductive Sciences).  Prof. Bukusi, in collaboration with Dr. Craig Cohen at UCSF, established the KEMRI Research Care and Training Program in 1995.

In addition to her substantial experience in conducting socio-behavioral and biomedical research and providing HIV care, mentoring and training health care and research personnel to enhance local and international capacity, she has a strong interest in research and clinical ethics and the development of systems and structures for regulation of research at KEMRI and in the country. She is the chairperson of the National Bioethics Society of Kenya, (BSK), a multidisciplinary, non-political, non-discriminatory, and not-for-profit organization with a primary objective to promote high ethical standards in bio-medical research, medicine and health care in Kenya. She is a board member of AVAC, Chaired the WHO HRP Alliance (capacity building for RH research) 2016 to 2021, and is a trustee for the HIV Trust, and an Elected Fellow of the African Academy of Sciences (FAAS).

Academic/Professional Qualifications
1981-  1987 Faculty of Medicine, University of Nairobi Bachelor of Medicine and Bachelor of surgery
2012- 2014


Centre for Biomedical Ethics and Culture, Sind Institute of Urology and Transplantation Masters in Bioethics (MBE), Karachi


University of Cape, Town Post Graduate Diploma in International Research Ethics, Cape Town
2001-2006 Department of Epidemiology, School of Public Health, University of Washington PhD (Epidemiology), Washington, Seattle


Department of Health Services, University of Washington, Seattle Certificate in International Health, Washington, Seattle

Department of Epidemiology, University of Washington, Seattle Master of Public Health (Epidemiology), Washington, Seattle

1990 -1995 Department of Obstetrics and Gynecology, Faculty of Medicine University of Nairobi. Masters of Medicine in Obstetrics and Gynecology, Nairobi


Other Trainings

Oct -Dec 2020 Practitioner Diploma in Executive Coaching
Aug – Oct 2016 Strategic Leadership Development Programme (SLDP), Kenya School of Government
Sept 2014 Primary Responsibility in Medicine and Research CIP (Certified IRB Professional
April 2014 University of Washington – Leadership and Management in Health
Sept 2011 Research Ethics Training Initiative (SARETI) Module on Institutionalizing Ethical Review of Health Research and Ethical Issues in HIV Prevention Trials, University of KwaZulu-Natal, Pietermaritzburg, South Africa
Sept 2008 Leadership Training, Haggai Institute Hawaii, USA


October 2007 Training on Data and Safety Monitoring for African Institutions, Dar es Salaam, Tanzania
January 2003 Good Clinical Practice: African International Clinical Sciences Workshop Mtubatuba, South Africa
August 2002 Project Management, British Council, Nairobi, Certificate Nairobi
March 1997 WHO Regional Reproductive Epidemiology Workshop (INCLEN/ Dept of Obs/ Gyn, UON) Nairobi
June 1995 Principles of HIV and STD Research University of Washington, Seattle, US
March 1995 Care and Counseling of the terminally ill patients. Nairobi Hospice, Nairobi
April 1994 Basic course in laparoscopy for family planning JHPIEGO/Department of Obs/Gyn, UON. Nairobi
1993 Case-control studies, evaluation and management. FHI/Dept of Obs/Gyn Nairobi


Selected Publications
  1. Zamudio-Haas S, Auerswald C, Miller L, Amboka S, Agot I, Kadede K, Otieno B, Odhiambo H, Odeny D, Onyango J, Bukusi EA, Truong HM Seeking a “Sponyo”: Insights Into Motivations and Risks Around Intergenerational Transactional Sex Among Adolescent Boys and Girls in Kenya. J Adolesc Health. 2021 May;68(5):930-936. doi: 10.1016/j.jadohealth.2020.09.027. Epub 2020 Nov 18.PMID: 33221187
  2. Anderson JL, Li P, Bukusi EA, Darbes LA, Hatcher AM, Helova A, Kwena ZA, Musoke PL, Owino G, Oyaro P, Rogers AJG, Turan JM Effects of a Home-Based Intervention on HIV Prevention Health Behaviors in Pregnant/Postpartum Kenyan Women: Estimating Moderating Effects of Depressive Symptoms..AIDS Behav. 2021 Apr;25(4):1026-1036. doi: 10.1007/s10461-020-03046-2. Epub 2020 Oct 14.PMID: 33057976 Clinical Trial.
  3. Hatcher AM, Weiser SD, Cohen CR, Hagey J, Weke E, Burger R, Wekesa P, Sheira L, Frongillo EA, Bukusi EA Food Insecurity and Intimate Partner Violence Among HIV-Positive Individuals in Rural Kenya..Am J Prev Med. 2021 Apr;60(4):563-568. doi: 10.1016/j.amepre.2020.06.025. Epub 2020 Oct 1.PMID: 33012622
  4. Hampanda K, Helova A, Odwar T, Odeny T, Onono M, Bukusi E, Turan J, Abuogi L.Male partner involvement and successful completion of the prevention of mother-to-child transmission continuum of care in Kenya. Int J Gynaecol Obstet. 2021 Mar;152(3):409-415. doi: 10.1002/ijgo.13442. Epub 2020 Dec 10.PMID: 33108671
  5. Truong HM, Mocello AR, Ouma D, Bushman D, Kadede K, Ating’a E, Obunge D, Bukusi EA, Odhiambo F, Cohen CR Community-based HIV testing services in an urban setting in western Kenya: a programme implementation study. .Lancet HIV. 2021 Jan;8(1):e16-e23. doi: 10.1016/S2352-3018(20)30253-8. Epub 2020 Nov 6.PMID: 33166505
  6. Irungu EM, Ngure K, Mugwanya KK, Awuor M, Dollah A, Ongolly F, Mugo N, Bukusi E, Wamoni E, Odoyo J, Morton JF, Barnabee G, Mukui I, Baeten JM, O’Malley G; Partners Scale-Up Project Team “Now that PrEP is reducing the risk of transmission of HIV, why then do you still insist that we use condoms?” the condom quandary among PrEP users and health care providers in Kenya. AIDS Care. 2021 Jan;33(1):92-100. doi: 10.1080/09540121.2020.1744507. Epub 2020 Mar 24.PMID: 32207327
Academic/ Professional Qualifications
  • PhD (Microbiology)

Dr. John Mwaniki Njeru

Principal Research Scientist

Dr. Mwaniki is a Medical microbiologist by training. His current scientific research interests are microbiology and Antimicrobial Resistance (AMR) surveillance, development of rapid point of care diagnostic tools (POCT), and elucidating the molecular epidemiology of (Re)-Emerging infectious diseases.

As the PI or Co-PI, he has collaborated/ is collaborating with scientists in Kenya and outside Kenya in research projects focusing on understanding the epidemiology of Neglected Zoonotic Diseases (Q fever, Campylobacteriosis, Brucellosis, Tularemia, Anthrax, relapsing fever) and SARS-COV2, and their relative contributions in causing diseases or outbreaks in Kenya, risk factors involved in the transmission and investigation the drivers for emergence and transmission of antibiotic resistance in selected common bacterial pathogens. Additionally, Dr. Mwaniki is involved in developing and validating novel POCT for rapid detection of the epidemic or Louse-borne relapsing fever (LBRF) caused by the bacterium Borrelia recurrentis.

The overall goal is to provide the best scientific-based evidence essential for:

  • Appropriate policy formulations towards cost-effective control strategies for these diseases and AMR, and
  • The development of sensitive and specific rapid affordable diagnostic methods applicable in resource-limited settings.
Current Fellowships
  1. February 2020: Research Fellow at the One Health Regional Network for the Horn of Africa (HORN) held at International Livestock Research Institute (ILRI). (Click Here)
  2. September 2019: Research fellow at the  LOEWE-Centre DRUID consortium held at the University of Giessen. (Click Here)
Selected Pulications
  1. John Njeru. Emerging carbapenem resistance in ESKAPE organisms in sub-Saharan Africa and the way forward. J. Microbiol. 2021. vol. 1(1) 3-6(View)
  2. Klemmer J, Njeru J, Emam A, El-Sayed A, Moawad AA, Henning K, et al. 2018. Q fever in Egypt: Epidemiological survey of Coxiella burnetii specific antibodies in cattle, buffaloes, sheep, goats and camels. PLoS ONE 13(2): e0192188. (View)
  3. Njeru J, Tomaso H, Mertens K, Henning K, Wareth G, Heller R, Kariuki S, Fèvre E, Neubauer H, Pletz M: Serological evidence of Francisella tularensis in febrile patients seeking treatment at remote hospitals, Northeastern Kenya, 2014-2015. New Microbes and New Infections; 19: 62–66; doi: 10.1016/j.nmni.2017.05.015. (View)
  4. de Glanville WA, Conde-A´lvarez R, Moriyo´n I, Njeru J, Dı´az R, Cook EAJ, et al. Poor performance of the rapid test for human brucellosis in health facilities in Kenya. PLoS Neglected Tropical Diseases. 11(4): e0005508. (View)
  5. Njeru J, Henning K, Pletz MW, Heller R, Forstner C, Kariuki S, Fèvre EM, Neubauer H. Febrile patients admitted to remote hospitals in Northeastern Kenya: seroprevalence, risk factors and a clinical prediction tool for Q Fever. BMC Infectious Diseases, doi: 10.1186/s12879-016-1569 (View)
  6. Njeru J, Melzer F, Wareth G, El-Adawy H, Henning K, Pletz MW, Heller R, Kariuki S, Fevre E, Neubauer H. Human Brucellosis in Febrile Patients Seeking Treatment at Remote Hospitals, Northeastern Kenya, 2014-2015. Emerging infectious diseases, 22(12):2160-64. doi: 10.3201/ eid2212. 160285. (View
  7. Nguyen TNM, Hotzel H, Njeru J, Mwituria J, El-Adawy H, Tomaso H, Neubauer H, Hafez HM. Antimicrobial resistance of Campylobacter isolates from small scale and backyard chicken in Kenya. Gut Pathogens, 8(1):39. (View)

Dr. Cecilia Mbae

Senior Research Scientist

Dr. Cecilia Mbae joined the Kenya Medical Research Institute in June 2004, as a Research Officer in the area of parasitology, and since then, she has been involved in several research projects on infectious diseases, either as a co-investigator or as a Principal Investigator, with funding from NIH, DFG, Wellcome trust among others.

Dr. Cecilia Mbae holds a basic degree in Zoology/Biochemistry, with an MSc in Medical parasitology and PhD in Life and molecular sciences from Open University, UK. Over the past 18 years, Dr Mbae’s research has focused on epidemiologic characterization of parasitic and bacterial enteric infections outbreak, utilizing basic  and molecular based methods to better understand ecology, transmission pathways and antimicrobial resistance of parasitic and bacterial pathogens. Some of the major pathogens of public health significance include Cryptosporidium spp, Giardia spp, Echinococcus spp, Salmonella typhi, invasive non-typhoidal salmonella, Vibrio cholera, E. coli among others that are endemic in our settings. All the studies have involved working closely with the communities, healthcare facilities for patient recruitment, and laboratory processes, and have been done through international collaborations.

Most of the studies Dr. Mbae has been involved in have had an impact in communities through feedback and dissemination meetings at community level and offering community-based interventions. Data collected from these studies have contributed to policy change in control, treatment and management of food and water borne infections as well as neglected infections.

Currently, Dr. Mbae is mentoring several undergraduate, post graduate students and junior scientists, and supervised/trained more than 10 Msc and 3 PhD students. She has authored/ co-authored more than 30 manuscripts in peer reviewed journals. In Addition, Dr. Mbae is a faculty member at the KEMRI Graduate School.

Over and above, Dr. Mbae has participated in several regional and international conferences to disseminate research findings.

Selected Publications
  1. Schola K. Peter, Peter SK, Mutiso JM, Ngetich M, Mbae C, Kariuki S (2023) Seroprevalence of non-typhoidal Salmonella disease and associated factors in children in Mukuru settlement in Nairobi County, Kenya. PLoS ONE 18(7): e0288015. https://doi.org/ 10.1371/journal.pone.0288015
  2. Erastus Mulinge, Eberhard Zeyhle, Cecilia Mbae,  Lucy Gitau, Timothy Kaburu, Japhet Magambo, Ute Mackenstedt, Thomas Romig,  Peter Kern, Marion Wassermann. Cystic echinococcosis in donkeys in eastern Africa, Parasitology DOI: 10.1017/S0031182023000173
  3. Samuel Kariuki, Kelvin Kering, Celestine Wairimu, Robert Onsare, Cecilia Mbae Antimicrobial Resistance Rates and Surveillance in Sub-Saharan Africa: Where Are We Now? Infection and Drug Resistance 2022:15 3589–3609
  4. Kariuki S, Dyson ZA, Mbae C, Ngetich R, Kavai SM, Wairimu C, Anyona S, Gitau N, Onsare RS, Ongandi B, Duchene S, Ali M, Clemens JD, Holt KE, Dougan G. Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya. Elife. 2021 Sep 13;10:e67852. doi: 10.7554/eLife.67852.PMID: 34515028
  5. Kariuki S, Wairimu C, Mbae C. J Infect Dis. 2021 Dec 20;224(12 Suppl 2):S883-S889. doi: 10.1093/infdis/jiab457.PMID: 34550365Antimicrobial Resistance in Endemic Enteric Infections in Kenya and the Region, and Efforts Toward Addressing the Challenges.
  6. Erastus Mulinge, Cecilia Mbae, Benjamin Ngugi, Tabitha Irungu, Elizabeth Matey, Samuel Kariuki. Entamoeba species infection in patients seeking treatment for diarrhea and abdominal discomfort in Mukuru informal settlement in Nairobi, Kenya. Food and Waterborne Parasitology 23 (2021) e00122
  7. Cecilia Kathure Mbae, Ph.D; Moses Mwangi, MSc; Naomi Gitau, Msc; Tabitha Irungu; Fidelis Muendo; Zilla Wakio; Ruth Wambui; Susan Kavai, Msc; Robert Onsare; Celestine Wairimu; Ronald Ngetich; Frida Njeru; Sandra Van Puyvelde; John Clemens; Gordon. Dougan; Samuel Kariuki. Factors associated with occurrence of invasive Salmonella infections among children living in Mukuru slum, an urban informal settlement in Kenya. BMC Infectious Diseases (2020) 20:422 https://doi.org/10.1186/s12879-020-05134-z
  8. Samuel Kariuki; Cecilia Mbae; Sandra Van Puyvelde; Robert Onsare; Susan Kavai; Celestine Wairimu; Ronald Ngetich; John Clemens; Gordon Dougan. High relatedness of invasive multi-drug resistant non-typhoidal Salmonella genotypes among patients and asymptomatic carriers in endemic informal settlements in Kenya” PLoS Negl Trop Dis. 2020 Aug 3;14(8):e0008440. doi: 10.1371/journal.pntd.0008440. eCollection 2020 Aug

Dr. Robert Onsare

Senior Research Scientist

Dr. Onsare’s research interests revolve aroung whole-genome based characterization (Genomics), Antimicrobial Resistance, Immunology and Epidemiology of Nontyphoidal Salmonella (NTS) and Typhoid fever and other key tropical enteric bacteria including Shigella spp, Vibrio cholerae and Escherichia coli.

Academic and Professional Qualifications

Dr. Onsare holds a Ph.D. in Medical Microbiology from Jomo Kenyatta University of Technology (JKUAT) (2015) Novartis Vaccines Institute for Global Health, Italy (Currently GSK Vaccines Institute for Global Health). He also holds a Master of Science in Medical Microbiology, from JKUAT in 2010

Selected Publications
  1. Onsare, R. S. & Maclennan, C. A. 2014. New genomics studies to understand the link between nontyphoidal Salmonella bacteremia and gastroenteritis in Africa. J Infect Dev Ctries, 8, 252-3.
  2. Onsare, R. S., Micoli, F., Lanzilao, L., Alfini, R., Okoro, C. K., MuigaI, A. W., Revathi, G., Saul, A., Kariuki, S., Maclennan, C. A. & Rondini, S. 2015. Relationship between Antibody Susceptibility and Lipopolysaccharide O-Antigen Characteristics of Invasive and Gastrointestinal Nontyphoidal Salmonellae Isolates from Kenya. PLoS Negl Trop Dis, 9.
  3. Kariuki, S & Onsare, R. S. (2015). Epidemiology and Genomics of Invasive Nontyphoidal Salmonella Infections in Kenya. Clinical Infectious Diseases, vol. 61 Suppl 4, pp. S317-24.
  4. Kariuki, S., Onsare, R., Mwituria, J., Ngetich, R., Nafula, C., Karimi, K., KarimI, P., Njeruh, F., Irungu, P. & Mitema, E. 2013. Improving food safety in meat value chains in Kenya. General interest paper: FAO/WHO project report.
Academic/ Professional Qualifications
  • Bachelors degree in Medicine and Surgery (MBChB)
  • Master of Science in clinical research: the University of Liverpool PhD in Global Health Sciences

Dr. Maricianah Onono

Senior Research Scientist

Maricianah Atieno Onono (MBChB MSc PhD) is a medical doctor and senior principal clinical research scientist at Kenya Medical Research Institute Centre for Microbiology Research.  She is also an honorary lecturer and student research supervisor with Maseno University and the KEMRI Graduate school. She earned her medical degree from the University of Nairobi, her MSC in clinical research from the University of Liverpool and her PhD in Global Health Sciences from the University of California San Francisco.

Dr. Maricianah has extensive experience in public health research and mixed methods research methodologies. She has spent more than 15 years working in:

  1. Sexual reproductive, adolescent and child health research.
  2. Mental health
  3. Disease surveillance and public health
  4. Household water and food insecurity in Kenya as a medical practitioner and as a clinical research scientist.

Her work is highly multidisciplinary and collaborative in nature, as reflected in the breadth of research questions and methods, diversity of funding sources (NIH; UNICEF; WHO; Bill & Melinda Gates Foundation) and a number of collaborators (at least a dozen in the past five years). Her overarching research goal: to improve the health of the most vulnerable populations in sub-Saharan Africa.  She brings a proven track record of management and leadership of high-performance research teams and has conducted nearly 30 successful projects including large implementation science projects that leveraged both technology and community health workers (e.g. Mobile phone-enhanced integrated Community Case Management of Pneumonia, Malaria, and Diarrhea in Children under 5 years in Homa Bay County, Kenya; role PI), multi-site randomized controlled trials that contributed to global policy changes (The Evidence for Contraceptives options and HIV Outcomes (ECHO) Trial: A Multi Center, Open-Label, Randomized Clinical Trial Comparing HIV Incidence and Contraceptive Benefits in Women using Depot Medroxyprogesterone Acetate (DMPA), Levonorgestrel (LNG) Implant, and Copper Intrauterine Devices (IUDs); role Co-PI), as well as molecular and biological mechanisms studies that involved developing internal laboratory infrastructures and capacities (Effects of hormonal contraceptives on genital immunity and HIV susceptibility; role site PI).

She is currently the country director and site PI for the Single-dose HPV catch-up vaccination efficacy: A blinded, randomized study of single-dose HPV vaccination among adolescent girls and young women in Kenya. In this role she coordinates community, clinical, research and laboratory services across Nairobi, Thika, Kisumu and Mombasa as well as provide training and mentorship to junior scientists. Lastly, I have substantial experience in policy advocacy and analysis. She has evaluated priority setting and political prioritization for adolescent sexual reproductive health and served on several national technical working groups (TWG) including family planning TWG, PMTCT TWG and child health TWG resulting in changes in national guidelines for RH-HIV integration, integrated community case management and in changes in pneumonia treatment for sick children under 5-years.

Selected Publications

Most relevant recent publications related to the “Advancing Public Health in Kenya” (Selected from over 70) peer-reviewed publications include:

    1. Onono M, Odwar T, Wahome S, et al. Behavioral interventions can mitigate adverse pregnancy outcomes among women conceiving on antiretroviral therapy (ART) and those initiated on ART during pregnancy: Findings from the MOTIVATE trial in southwestern Kenya. Journal of Acquired Immune Deficiency Syndromes 2020 Oct. DOI: 10.1097/qai.0000000000002521 PMID: 33027156
    2. Maricianah Onono, Kavita Nanda, Kate B. Heller, Doug Taylor, Irina Yacobson, Renee Heffron, Margaret Phiri Kasaro, Cheryl E. Louw, Zelda Nhlabasti, Thesla Palanee-Phillips, Jenni Smit, Imelda Wakhungu, Peter B. Gichangi, Nelly R. Mugo, Charles Morrison, Jared M. Baeten (2020). Comparison of pregnancy incidence among African women in a randomized trial of intramuscular depot medroxyprogesterone acetate (DMPA-IM), a copper intrauterine device (IUDs), or a levonorgestrel (LNG) implant for contraception, for the Evidence for Contraceptive Options and HIV Outcomes (ECHO) Trial Consortium, Contraception  23 May 2020 PMCID: PMC7301167
    3. Onono MA, Brindis CD, White JS, Goosby E, Okoro DO, Bukusi EA, Rutherford GW. Challenges to generating political prioritization for adolescent sexual and reproductive health in Kenya: A qualitative study. PloS One. 2019 Dec 19;14(12):e0226426. PMCID: PMC6922405.
    4. Onono M, Abdi M, Opondo I, Okung’u J, Asadhi E, Nyamai R, Karimurio L, Okoth P, Qazi SA. Using the RE‐AIM framework to evaluate the implementation of integrated community case management in Kenya. Acta Paediatrica. 2018 Dec;107:53-62. DOI: 10.1111/apa.14405  PMID: 30570791

Find the complete List of Published Work (74) by Dr Onono in her Bibliography: (Click Here)

Dr. Erastus Mulinge Kakundi

Senior Research Scientist

Dr. Mulinge’s research interests span across disease surveillance and diagnostics, One Health, and molecular epidemiology of emerging and re-emerging zoonotic parasitic diseases. My research has focused on the molecular epidemiology of cryptosporidiosis, giardiasis, amoebiasis, and cystic echinococcosis in humans, domestic and wild animals.

Currently, Dr. Mulinge is involved in the following projects:

  1. Surveillance and epidemiological evaluation of COVID-19 in Kenya
  2. One Health intervention project at Oloisukut Conservancy in the Greater Mara Ecosystem, Kenya
  3. Epidemiology and clinical implications of the genetic diversity of Echinococcus spp. in Kenya
Academic and Professional Qualifications
  • PhD (Applied Parasitology), University of Nairobi 2020. Title of thesis: Molecular epidemiology of Echinococcus and Taenia species in dogs from cystic echinococcosis endemic areas in Kenya
  • Master of Science (Biochemistry), University of Kwa-Zulu Natal, South Africa, 2009. Title of thesis: Molecular analysis of Congopain gene family.
  • Bachelor of Science Hons (Biochemistry), Kenyatta University, 2001.
Selected Publications
  1. Mulinge, E., Mbae, C., Ngugi, B., Irungu, T., Matey, E., Kariuki, S. (2021). Entamoeba species infection in patients seeking treatment for diarrhoea and abdominal discomfort in Mukuru informal settlement in Nairobi, Kenya. Food Waterborne Parasitol. 23 (2021) e00122.
  2. Mulinge, E., Odongo, D., Magambo, J., Njenga, S., Zeyhle, E., Mbae, C., Kagendo, D., Addy, F., Ebi, D., Wassermann, M., Kern, P., Romig, T. (2020). Diversity of Taenia and Hydatigera (Cestoda: Taeniidae) in domestic dogs in Kenya. Parasitol. Res. 119(9):2863-2875.
  3. Mulinge, E., Magambo, J., Odongo, D., Njenga, S., Zeyhle, E., Mbae, C., Kagendo, D., Addy, F., Ebi, D., Wassermann, M., Kern, P., Romig, T. (2018). Molecular characterization of Echinococcus species in dogs from four regions of Kenya. Vet. Parasitol. 255, 49-57.
  4. Mbae, C., Mulinge, E., Guleid, F., Wainaina, J., Waruru, A., Njiru, Z.K., Kariuki, S. (2016). Molecular characterization of Giardia duodenalis in children in Kenya. BMC Infect. Dis. 16, 135.
  5. Kang’ethe, E.K., Mulinge, E.K., Skilton, R.A., Monda, J.G., Nyongesa, C.N., Mbae, C.K., Kamwati, S.K. (2012). Cryptosporidium species detected in calves and cattle in Dagoretti, Nairobi, Kenya. Trop. Anim. Health. Prod. Suppl. 1, 25-31.
  6. Gatei, W., Wamae, C.N., Mbae, C., Waruru, A., Mulinge, E., Waithera, T., Gatika, S.M., Kamwati, S.K., Revathi, G. and Hart, C.A. (2006). Cryptosporidiosis: prevalence, genotype analysis, and symptoms associated with infections in children in Kenya. Am. J. Trop. Med. Hyg. 75(1):78-82.

Dr. Lillian Musila

Principal Research Scientist

Dr. Musila is a biomedical research scientist with two decades of international research, academic and teaching experience in microbiology, parasitology, human genetics, cancer, virology, and molecular biology. She is devoted to developing quality research programs, health-science professionals, and policies to promote One Health research and provide innovative interventions and diagnostics to the challenges of infectious diseases and antimicrobial resistance.

Dr. Musila has worked at KEMRI/USAMRD-A for thirteen years in infectious disease surveillance and research on arboviral and bacterial pathogens. She is currently the principal investigator of the antimicrobial resistance program at USAMRD-A, Kenya. The program has several objectives:

  1. Conduct antimicrobial resistance surveillance to define patterns and track antibiotic resistance trends
  2. Investigate genetic determinants of resistance and virulence
  3. Determines the transmission patterns of multidrug-resistant bacterial pathogens between human, environmental, and animal reservoirs
  4. Identify bacteriophages that can treat infections caused by MDR bacterial pathogens.
Academic/Professional Qualifications

Dr. Musila has two postdoctoral fellowships from the National Laboratory Health Services in South Africa and Emory   University in Atlanta, GA, USA. She earned a Ph.D. in Molecular Parasitology from the University of Pennsylvania, Philadelphia, PA, USA, and a B.Sc. Microbiology from the University of Massachusetts, Amherst, MA, USA. She did her O- and A-level at Alliance Girls High School, Kenya.

In addition, she has Certificates of Epidemiology in Infectious Diseases Research from the University of Florida and  Leadership and Management in Health from the University of Washington.

Selected Publications
  1. Muriuki CW, Ogonda LA, Kyanya C, Matano D, Masakhwe C, Odoyo E, Musila L. Phenotypic and Genotypic Characteristics of Uropathogenic Escherichia coli Isolates from Kenya. Microb Drug Resist. 2021 Jul 23. (View)
  2. Odoyo E, Matano D, Georges M, Tiria F, Wahome S, Kyany’a C, Musila L. Ten Thousand-Fold Higher than Acceptable Bacterial Loads Detected in Kenyan Hospital Environments: Targeted Approaches to Reduce Contamination Levels. Int J Environ Res Public Health. 2021 Jun 25;18(13):6810. (View)
  3. Detection of diverse carbapenem and multidrug resistance genes and high-risk strain types among carbapenem non-susceptible clinical isolates of target gram-negative bacteria in Kenya. Musila L, Kyany’a C, Maybank R, Stam J, Oundo V, Sang W (2021) PLoS ONE 16(2): e0246937. (View)
  4. Colistin Resistance Gene mcr-8 in a High-Risk Sequence Type 15 Klebsiella pneumoniae Isolate from Kenya. Kyany’a C, Musila L. Microbiol Resour Announc. 2020 Sep 24;9(39):e00783-20. (View)
  5. Phenotypic and genotypic characterization of clinical Staphylococcus aureus isolates from Kenya Cecilia Kyany’ a Justin Nyasinga, Daniel Matano, Valerie Oundo, Simon Waciira, Willie Sang and Lillian Musila BMC Microbiology (2019):19:245 (View)
  6. A six-member SNP assay on the iPlex MassARRAY platform provides a rapid and affordable alternative for typing major African Staphylococcus aureus types.  Nyasinga J, Kyany’ a C, Okoth R, Oundo V, Matano D, Wacira S, Sang W, Musembi S, Musila L. Nyasinga, et al., Access Microbiology 2019;1-8 (View)

Dr. Benjamin Mbiyu Ngugi

Senior Principal Clinical Research Scientist

Dr. Benjamin M. Ngugi, MBChB (UoN), M.Phil. (Cambridge), ATCR (UCSF), PhD (JKUAT), is a medical doctor and a Doctor of Philosophy (Epidemiology) graduate from Jomo Kenyatta University of Agriculture and Technology (June, 2012). Previously, he attended Advanced Training in Clinical Research at the University of California, San Francisco (UCSF) from 2007 to 2008. He also holds a Master of Philosophy (Epidemiology) degree from the University of Cambridge, UK (2003), and a Bachelor of Medicine and Surgery degree from the University of Nairobi (1999). He is a Clinical Research Scientist at the Centre for Microbiology Research (CMR) in KEMRI, Nairobi.

Dr. Ngugi has headed the CMR Laboratory Services Project (CMR-LSP), previously the Hospitality Industry Support Program (HISP)) – a KEMRI revenue generation (RG) project for the last 12 years (since 2009). This program has in that time medically examined and certified over 200,000 food handlers within Nairobi and its environs. The program laboratories also carry out other laboratory work including COVID-19 testing for food handlers and for international travel.

Dr. Ngugi is also a Lecturer at the KEMRI Graduate School mainly teaching Epidemiology since 2011. In 2020 during the KEMRI’s 40th-anniversary celebrations he was recognised with an award (Certificate of Excellent Service) for the Best Lecturer at the KEMRI Graduate School.

Academic and Professional Qualifications
1992-1999 Faculty of Medicine, University of Nairobi Bachelor of Medicine and Bachelor of Surgery (MB.ChB.)
2001-2003 University of Cambridge, UK – Master of Philosophy in Epidemiology (M.Phil.)
2007-2008 University of California, San Francisco, USA –  Advanced Training in Clinical Research (ATCR-Cert.)
2007-2012 Jomo Kenyatta University of Science and Technology (JKUAT), Kenya – Doctor of Philosophy in Epidemiology
Selected Publications
  1. Ngugi BM, Hemmerling A, Bukusi EA, Kikuvi G, Gikunju J, Shiboski S, Fredricks DN and Cohen RC. Effects of BV-Associated Bacteria and Sexual Intercourse on Vaginal Colonization with the Probiotic Lactobacillus crispatus CTV-05. Sex. Trans. Dis. 2011
  2. Mbae C, Mulinge E, Waruru A, Ngugi B, Wainaina J, Kariuki S. Genetic diversity of Cryptosporidium in children in an urban informal settlement of Nairobi, Kenya. PLoS One. 2015;10(12):e0142055.
  3. Mary A. Uyoga, Simon Karanja, Daniela Paganini, Colin I. Cercamondi, Sophie A. Zimmermann, Benjamin Ngugi, Penny Holding, Diego Moretti, Michael B. Zimmermann. Duration of exclusive breastfeeding is a positive predictor of iron status in 6- to 10-month-old infants in rural Kenya. Maternal & Child Nutrition. 2016
  4. BN Lowoko, BM Ngugi, A Malal and JK Mutai. Factors Associated With Intestinal Parasites Among School Going Children in Lodwar Municipality, Turkana County, Kenya. East African Medical Journal Vol. 91 No. 1 January 2017
  5. DM Miriti, GM Kikuvi, BM Ngugi and DG Magu. Oral Health Status and its Associated Factors among the Youth in Igembe Sub-County, Meru County. Journal of Health, Medicine and Nursing ISSN 2520-4025 (Online) Vol.5, Issue 1. No.3, pp 33- 47, 2020
  6. Erastus Mulinge, Cecilia Mbae, Benjamin Ngugi, Tabitha Irungu, Elizabeth Matey and Samuel Kariuki. Entamoeba species infection in patients seeking treatment for diarrhoea and abdominal discomfort in Mukuru informal settlement in Nairobi, Kenya. Food and Waterborne Parasitology 23 (2021) e00122.

Dr. Richard Kipserem Korir

Senior Research Officer

Dr. Korir is a senior research scientist and head of OI Unit at CMR-KEMRI. As a researcher, Dr. Korir has written twenty proposals, of which 10 have been funded as well as published 22 papers in peer-reviewed journals with 7 as a first author.

Dr. Korir has fifteen years of research experience with expertise in bacteriology/mycology, molecular microbiology, drugs development from natural products and antimicrobial resistance.

Academic and Professional Qualifications
  • Doctor of Philosophy degree in Medical Microbiology.
  • Master of Science degree in Medical Microbiology.
  • Bachelor of Science degree in Biological Science.
Selected Publications
  1. Ruth MonyenyeNyangacha, David Odongo, Florence Oyieke, MissianiOchwoto, Richard Korir, Ronald Kiprotich Ngetich, Gladys Nginya, OlipherMakwaga, Christine Bii, Peter Mwitari, Festus Tolo (2017). Secondary bacterial infections and antibiotic resistance among tungiasis patients in Western, Kenya. PLO Neglected Tropical Disease Journal (View)
  2. Richard Korir, OmuAnzala, Walter Jaoko, Christine Bii1and Lucia Keter (2017). Occurrence of Aflatoxins and Fumonisins Contamination in Herbal Medicinal Products Sold in Nairobi, Kenya. Food Science and Quality Management online journal, Vol 63, 2017
  3. Richard Korir, OmuAnzala, Walter Jaoko, Christine Biiand Lucia Keter(2017). Multi-Drug Resistant Bacteria Isolates Recovered from Herbal Medicinal Products in Nairobi Kenya – The East African Health Research Journal, 1(1): 41-46
  4. Keter L., Too, R., Mutai, C., Mwikwabe, N., Ndwigah, S., Orwa, J., Mwamburi, E. and Korir, K. (2016). Bacteria Contaminants and their Antibiotic Sensitivity from Selected Herbal Medicinal Products from Eldoret and Mombasa, Kenya. American Journal of Microbiology, 7(1): 18-28.
  5. Korir K.,Mutai C., Nandako J.and Bii C. (2012).Antimicrobial Properties of Hugoniacastaneifolia and Its Potential Use for the Control of Opportunistic Infections –East Africa Medical Journal Vol. 88 No.4
  6. Korir K. and Bii CC. (2012).Mycological Quality of Maize Flour from Aflatoxins “Hot” Zone Eastern Province – Kenya. – Afr J Health Sci. Volume 21: 3-4

Dr, James Ayieko - MBChB, MPH, PhD

Research Scientist

James Ayieko is a medical doctor who holds an undergraduate degree from Moi University, School of Medicine, an MPH from University of California, Berkeley and a PhD in Epidemiology from the University of Antwerp, Belgium.

James’ career over the last decade has centered around HIV care and ways of improving treatment outcomes in low resource settings as well as prevention of new infections. His area of interest has been improving treatment outcomes by optimizing the HIV care cascade right from linkage of HIV infected individuals to care, retention, viral suppression and HIV prevention for the uninfected. He has participated in designing, implementation and evaluation of various interventions aimed at optimizing delivery of prevention options such as PEP and PrEP in rural Uganda and Kenya.

Beyond HIV, he has also been involved in designing and implementation of Non-communicable disease studies such as Hypertension and alcohol dependence.  Currently he works with the Kenya Medical Research Institute (KEMRI) as a Clinical Research Scientist and is an investigator in a number of trials.

James is an Adjunct Lecturer at the Maseno University, School of Medicine, Department of Emergency Medicine and an External examiner at the University of Cape Town, South Africa, School of Public Health, Post graduate studies.

Selected Publications

He has over 45 publications in peer reviewed journals:

  1. Ayieko J, Petersen ML, Kamya MR, Havlir DV. PEP for HIV prevention: are we missing opportunities to reduce new infections? J Int AIDS Soc. 2022 May;25(5):e25942. PMID: 35633097; PMCID: PMC9142817. (View Publication)
  2. Ayieko J, Petersen ML, Charlebois ED, Brown LB, Clark TD, Kwarisiima D, Kamya MR, Cohen CR, Bukusi EA, Havlir DV, Van Rie A. A patient-centered multi-component strategy for accelerated linkage to care following community-wide HIV testing in rural Uganda and Kenya. J Acquir Immune Defic Syndr. 2018 Dec 20. doi: 10.1097
  3. Heller DJ, Balzer LB, Kazi D, Charlebois ED, Kwarisiima D, Mwangwa F, Jain V, Kotwani P, Chamie G, Cohen CR, Clark TD, Ayieko J, Byonanabye DM, Petersen M, Kamya MR, Havlir D, Kahn JG. Hypertension testing and treatment in Uganda and Kenya through the SEARCH study: An implementation fidelity and outcome evaluation. PLoS One. 2020 Jan 15;15(1):e0222801. doi: 10.1371/journal.pone.0222801. PMID: 31940346; PMCID: PMC6961918.
  4. Ayieko J, Chamie G, Balzer L, Kwarisiima D, Kabami J, Sang N, Cohen CR, Bukusi EA, Clark TD, Plenty A, Charlebois ED, Petersen M, Kamya M, Havlir DV, Ruel T. Mobile, Population-wide, Hybrid HIV Testing Strategy Increases Number of Children Tested in Rural Kenya and Uganda. Pediatr Infect Dis J. 2018 Dec;37(12):1279-1281. doi: 10.1097/INF.0000000000002142.
  5. Ayieko J, Brown L, Anthierens S, Van Rie A, Getahun M, Charlebois ED, Petersen ML, Clark TD, Kamya MR, Cohen CR, Bukusi EA, Havlir DV, Camlin CS. “Hurdles on the path to 90-90-90 and beyond”: Qualitative analysis of barriers to engagement in HIV care among individuals in rural East Africa in the context of test-and-treat. PLoS One. 2018 Aug 30;13(8):e0202990. doi: 10.1371/journal.pone.0202990. eCollection 2018.
  6. Ayieko J, Petersen ML, van Rie A, Wafula E, Opudo W, Clark TD, Kamya MR, Balzer LB, Cohen CR, Bukusi EA, Charlebois ED, Havlir DV. Effect of a Patient-Centered Phone Call by a Clinical Officer at Time of HIV Testing on Linkage to Care in Rural Kenya. Open Forum Infect Dis. 2018 May 29;5(6):ofy126. (View Publication)
  7. Ayieko J, Ti A, Hagey J, Akama E, Bukusi EA, Cohen CR, Patel RC. HIV status and treatment influence on fertility desires among women newly becoming eligible for antiretroviral therapy in western Kenya: insights from a qualitative study. Reprod Health. 2017 Aug 8;14(1):93. doi: 10.1186/s12978-017-0355-9.
Susa Kavai

Ms. Susan Kavai

Research Scientist

Susan Kavai obtained her BSc. and MSc. in Medical Microbiology at Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya. While there, she focused on Antimicrobial resistance of enteric food borne pathogens such as Salmonella spp and E. coli spp. She is currently a Research Scientist at Centre for Microbiology Research at the Kenya Medical Research Institute (KEMRI).

Her roles, duties and responsibilities include AMR surveillance, Quality laboratory  systems management, Data generation and management. She is currently a PhD student at the University of Nairobi pursuing a Doctorate in Tropical and infectious diseases.

Completed and ongoing projects
  1. Analysis of Trends and Genes Coding for Resistance to Fluoroquinolones and Extended Spectrum β-Lactams among Salmonella enterica Typhi Isolates Obtained from Patients in Nairobi County, Kenya (PI) P/NO: KEMRI/SERU/CMR/P00053/3469
  2. Evaluation of Usage and Management of Human and Veterinary Antimicrobials in Meru and Kwale County (CO-PI) P/NO KEMRI/IRG/012/2017/18
  3. Cholera Prevention, Preparedness, And Control In Kenya Through Hotspot Mapping, Genotyping, Exposure Assessment, And Wash + Oral Cholera Vaccine Interventions (CO-PI) P/NO: KEMRI/SERU/CMR/P00116/3871
  4. Epidemiology and Genomics of Multidrug Resistant Salmonella Typhi In Kenya: The Role of Carriage in Humans in an Endemic Settings P/NO: KEMRI/SERU/CMR/P00102/3781
  5. Salmonella Epidemiology and Genomics in endemic settings in Kenya P/NO SCC 2076
  6. Ecology and epidemiology of antimicrobial-resistant foodborne pathogens in selected sites in five Counties in Kenya: P/NO: KEMRI/SERU/CMR/P00036/3205
  7. Antimicrobial Resistance, Phylogenetic and Evolutionary Characterization of Salmonella enterica serovar Typhi in Disease and Carriage in Endemic Settings in Nairobi County, Kenya (PI) P/NO: KEMRI/SERU/CMR/P00150/4146
  8. Multidrug resistant invasive non-typhoidal Salmonella disease in children: The role of carriage in humans and environmental contamination in an endemic setting in Kenya (MISSIoN)P/NO: KEMRI/SERU/CMR/P00102/3781
Selected Publications
  1. Samuel Kariuki, Zoe A Dyson, Cecilia Mbae, Ronald Ngetich, Susan M Kavai, Celestine Wairimu, Stephen Anyona, Naomi Gitau, Robert Onsare, Beatrice Ongandi, Sebastian Duchene, Mohamed Ali, John Clemens, Kathryn E Holt, Gordon Dougan, Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya. (View Publication)
  2. Samuel Kariuki ,Cecilia Mbae,Sandra Van Puyvelde,Robert Onsare,Susan Kavai,Celestine Wairimu,Ronald Ngetich,John Clemens,Gordon Dougan; High relatedness of invasive multi-drug resistant non-typhoidal Salmonella genotypes among patients and asymptomatic carriers in endemic informal settlements in Kenya Published: August 3, 2020 (View Publication)
  3. Cecilia Mbae,Moses Mwangi,Naomi Gitau,Tabitha Irungu,Fidelis Muendo,Zilla Wakio,Ruth Wambui,Susan Kavai,Robert Onsare,Celestine Wairimu,Ronald Ngetich,Frida Njeru,Sandra Van Puyvelde,John Clemens,Gordon Dougan, Samuel Kariuki, Factors associated with occurrence of salmonellosis among children living in Mukuru slum, an urban informal settlement in Kenya. BMC Infectious Diseases ( IF 2.688 ) Pub Date : 2020-06-17 (View Publication)
  4. Samuel Kariuki, Cecilia Mbae,  Robert Onsare,  Susan M Kavai,  Celestine Wairimu, Ronald Ngetich,  Mohammad Ali,  John Clemens,  Gordon Dougan Multidrug-resistant Nontyphoidal Salmonella Hotspots as Targets for Vaccine Use in Management of Infections in Endemic Settings Clinical Infectious Diseases, Volume 68, Issue Supplement_1, 15 February 2019, Pages S10–S15, (View Publication)
  5. Kavai S, Kangogo M, Muigai A, Kariuki S: Analysis of Trends in Resistance to Fluoroquinolones and Extended Spectrum Beta-Lactams among Salmonella Typhi Isolates Obtained from Patients at Four Outpatient Clinics in Nairobi County, Kenya. Advances in Microbiology 2018, 8:578-588.
  6. Horace Gumba, Joseph Waichungo, Brett Lowe, Alfred Mwanzu, Robert Musyimi, Johnstone Thitiri, Caroline Tigoi, Martin Kamui, James A. Berkley, Ronald Ngetich, Susan Kavai, Samuel Kariuki; Implementing a quality management system using good clinical laboratory practice guidelines at KEMRI-CMR to support medical research Wellcome Open Research2018 vol: 3  (View Publication)

Ms. Susan Wambui Kiiru

Research Scientist.

Susan is a Molecular Microbiologist at the centre for Microbiology Research for 5 years and a research scientist at the Centre for Virus Research. She is a course assistant at the Wellcome Trust Advanced Courses (WTAC).

Ms. Kiiru has been involved in workshops on laboratory isolation, antibacterial susceptibility testing, and molecular characterization of foodborne bacteria using one health approach.

Academic/ Professional Qualifications
  • Masters in Medical Microbiology (ongoing)
  • Bsc in Molecular Cell Biology
Selected Publications
  1. Thuo, T. , Kiyuukia, C. , Maina, J. , Judah, T. , Kiiru, S. and Kiiru, J. (2019) Antimicrobial Resistance Profiles and Clonal Relatedness of Pseudomonas aeruginosa Strains Recovered from Wounds Infections of Outpatient Population Presenting in a Rural Hospital in Kenya. Advances in Microbiology9, 119-130. doi: (View)
  2. Maina, J. , Ndung’u, P. , Muigai, A. , Onyango, H. , Mukaya, J. , Wambui, S. , Judah, T. , Kinyua, J. , Muriuki, J. , Chesenge, L. , Kisoo, L. , Thuku, R. , Wachira, B. , Bett, V. , Gachuki, T. and Kiiru, J. (2019) Antimicrobial Profiles of Selected Gram-Negative Bacteria Recoverable from Sewage and Sludge from Juja and Kibera Informal Settlements of the Larger Nairobi Metropolis. Advances in Microbiology9, 507-524. doi: (View)

Tom Turbine Ouko

Chief Medical Laboratory Technologist

Mr. Ouko is a medical microbiologist heading laboratory services (CMR) with 13 technical personnel

He is a member of the CMR training committee and acting Secretary,  Centre Scientific Committee. Additionally, he is a member of the Kenya Medical Laboratory Technicians and Technologists Board (KMLTTB) and  American Society of Medical Microbiology

Mr. Ouko’s research interests are in molecular epidemiology of infectious diseases, drug resistance surveillance, control and management.

Selected Publications
  • PhD in Infectious Diseases and Vaccinology – Ongoing
  • MSc in Medical Microbiology
Selected Publications
  1. Ouko TT, Ngeranwa JN, Orinda GO, Bii CC, Amukoye E, Lucy M, Wamae CN Oxacillin resistant Staphylococcus aureus among HIV infected and non-infected patients in Kenya. East Afr Med. J. 2010; 87 (5).
  2. Talaam, KK, Kirui, MC, Nga’ng’a, ZW, Olga, M, Ouko, T and Bii, CC. Mycological quality of ‘Mursik’ Collected from Soliat Location, Kericho County, Kenya. African Journal of Health Sciences, Volume 27, Number 2, April-June 2014.
  3. C. Bii, Ouko TT, E. Amukoye, and L.W. Githinji (2002). Antifungal drug susceptibility of Candida albicans. East African Medical Journal. 79(3): 143-145.
  4. M. Chakaya, C. Bii, L. Ng’anga’, E. Amukoye, Ouko TT, L. Muita, S. Gathua, J. Gitau, Odongo, J.M. Kabanga, K. Nagai, S. Suzumura and Y. Sugiura. (2003). Pneumocystis Carinii pneumonia in HIV/AIDS patients at an Urban District Hospital in Kenya. East African Medical Journal. 80(1): 30-35.
  5. CC Bii, J. Kose, H. Taguchi, E. Amukoye, Ouko TT, Muita, O. Mugasia, NC Wamae, S. Kamiya. Pneumocystis jirovecii and microbiological findings in children with severe pneumonia in Nairobi, Kenya. International journal of tropical Lung Diseases 10(11):1286-1291.
  6. Bii CC, Taguchi H, Ouko TT, Mwita LW, Wamae N, Kamiya S. (2005) Detection of virulence related genes by multiplex PCR in multi-drug resistant Diarrheaogenic Escherichia coli isolates from Kenya and Japan. Epidemiology and Infection. 133(4):627-33
  7. Prevalence and risk factors for Campylobacter infection in diarrheal patients in Busia County, Kenya – PhD manuscript awaiting publication.
Academic and Professional Quaifications

B.Sc., M.Sc. in Medical Microbiology

Mr. John N Maina

Research scientist

Mr. Maina is a research scientist at the Center for Microbiology with 6 years of experience in Microbiology and Molecular Biology techniques.

During this period he has worked with various bacteriology and AMR research projects includes the Urban zoonosis, sewage metagenomics, Vibro cholerae and wild animal protection (WAP) project. currently, Mr Maina is involved in investigating drivers and the burden of AMR in Kenya as part of the HATUA consortium, an East African project that uses the One Health approach.

His research interest includes bacterial genomics, AMR in clinical and environmental bacterial pathogens.

Selected Publications
  1. Wanja, F. , Ngugi, C. , Omwenga, E. , Maina, J. and Kiiru, J. (2021) Urinary Tract Infection among Adults Seeking Medicare at Kiambu Level 5 Hospital, Kenya: Prevalence, Diversity, Antimicrobial Susceptibility Profiles and Possible Risk Factors. Advances in Microbiology, 11, 360-383. doi: 10.4236/aim.2021.118028. (View)
  2. Maina, John, Perpetual Ndung’u, Anne Muigai, and John Kiiru. “Antimicrobial resistance profiles and genetic basis of resistance among non-fastidious Gram-negative bacteria recovered from ready-to-eat foods in Kibera informal housing in Nairobi, Kenya.” Access Microbiology 3, no. 6 (2021): 000236. (View)
  3. Maina, J. N. (2020). Mapping the distribution patterns of multiple-drug resistances gram-negative bacterial strains recoverable from food and environmental samples in Kibera informal settlements.(View)
  4. Maina, J. , Ndung’u, P. , Muigai, A. , Onyango, H. , Mukaya, J. , Wambui, S. , Judah, T. , Kinyua, J. , Muriuki, J. , Chesenge, L. , Kisoo, L. , Thuku, R. , Wachira, B. , Bett, V. , Gachuki, T. and Kiiru, J. (2019) Antimicrobial Profiles of Selected Gram-Negative Bacteria Recoverable from Sewage and Sludge from Juja and Kibera Informal Settlements of the Larger Nairobi Metropolis. Advances in Microbiology, 9, 507-524. doi: 10.4236/aim.2019.96031. (View)
  5. Thuo, T. , Kiyuukia, C. , Maina, J. , Judah, T. , Kiiru, S. and Kiiru, J. (2019) Antimicrobial Resistance Profiles and Clonal Relatedness of Pseudomonas aeruginosa Strains Recovered from Wounds Infections of Outpatient Population Presenting in a Rural Hospital in Kenya. Advances in Microbiology, 9, 119-130. doi: 10.4236/aim.2019.92009. (View)
  6. A., Ngugi, C., Maina, J. and Kiiru, J. (2018) Urinary Tract Infection among Pregnant Women at Pumwani Maternity Hospital, Nairobi, Kenya: Bacterial Etiologic Agents, Antimicrobial Susceptibility Profiles and Associated Risk Factors. Advances in Microbiology, 8, 175-187. (View)